#!/usr/bin/env bash

ls $PWD/example/*.fastq.gz > example/reads.txt
TEspeX --TE example/ce.Dfam.fa.gz \
--cdna example/Caenorhabditis_elegans.WBcel235.cdna.all.fa.gz \
--ncrna example/Caenorhabditis_elegans.WBcel235.ncrna.fa.gz \
--sample example/reads.txt --paired F --length 50 --out test --strand no

diff test/outfile.txt example/outfile.txt
diff test/mapping_stats.txt example/mapping_stats.txt